Same problem, and went a bit further by excluding the package from the two fedora repos, that tries to downgrade it.
This will stop both dnf and PackageKit which Gnome-Software uses, from ever trying to downgrade using the official fedora repositories again.
Edit the following two files:
/etc/yum.repos.d/fedora.repo
/etc/yum.repos.d/fedora-updates.repo
If you use the updates-testing repo, remember to do it for that one as-well.
Add the following to both:
exclude=synergy
Example on how it looks in /etc/yum.repos.d/fedora-updates.repo for me:
[updates